Thanks for your opinion. I checked references and of course noticed that
both names already have a quite special meaning in the context of their
original usage, but also describe a general concept.
When using such a general concept, then it is not a good idea to
re-invent a name for that. My thinking is/was that while in SMD the main
concept is to find an energy difference between two states, in targeted
MD the main concept is to transform one structure to another.
With this simplistic view, I figured that targeted molecular dynamics
might be the better name for what we are doing.
Based on your opinion, I will reconsider... what is important in the end
is that we do not use a wrong name.
Cheers!
On 06/05/2013 09:59 AM, Daniel Sindhikara wrote:
> I believe the name targeted MD is already taken:
> Schlitter, J., et al. "Targeted molecular dynamics simulation of
> conformational change-application to the T↔ R transition in insulin."
> Molecular Simulation 10.2-6 (1993): 291-308.
>
> In my opinion, Steered MD might be better since although steered MD is
> often used with Jarzynski, it doesn't necessarily have to.
> But you should check the references.
>
> -Dan
>
>
>
> On Wed, Jun 5, 2013 at 4:16 PM, Jan-Philip Gehrcke
> <jgehrcke.googlemail.com>wrote:
>
>> Since there was no complaint, I guess it's fine to just call it targeted
>> molecular dynamics.
>>
>> On 06/01/2013 04:08 PM, Jan-Philip Gehrcke wrote:
>>> Hello,
>>>
>>> when we apply a time-dependent distance restraint between two atoms in
>>> an MD simulation with a priori defined start and end values, we can
>>> generally call this targeted molecular dynamics, can't we? I want to
>>> avoid 'steered molecular dynamics' since in literature this term seems
>>> to implicate the evaluation of the force-time relationship via the
>>> Jarzynski equality, which we do not do.
>>>
>>> General advice on how to call such an MD (common MD with additional
>>> time-dependent distance restraint between two atoms) in a manuscript
>>> title is welcome.
>>>
>>> Thanks,
>>>
>>> Jan-Philip
>>>
>>
>>
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>
>
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Received on Wed Jun 05 2013 - 03:30:03 PDT
